Permeation of small molecules through a lipid bilayer: a computer simulation study
Bemporad, Daniele, Essex, Jonathan W. and Luttmann, Claude (2004) Permeation of small molecules through a lipid bilayer: a computer simulation study. Journal of Physical Chemistry B, 108, (15), 4875-4884. (doi:10.1021/jp035260s)
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Official URL: http://dx.doi.org/10.1021/jp035260s
Description/Abstract
To reach their biological target, drugs have to cross cell membranes, and understanding passive membrane permeation is therefore crucial for rational drug design. Molecular dynamics simulations offer a powerful way of studying permeation at the single molecule level, yielding detailed dynamic and thermodynamic data. Biological membranes have a very inhomogeneous character and a highly anisotropic behavior. Starting from a computer model proven to reproduce the physical properties of such a complex system, the permeation of small organic molecules across a lipid bilayer model has been studied. Free energy profiles and diffusion coefficients along the bilayer normal have been calculated for small organic molecules by means of all-atom molecular dynamics (MD) simulations constraining the compounds at chosen depths inside the membrane. These data also allow for the calculation of permeability coefficients, the results for which have been compared with experimental data. The calculated permeability coefficients are generally 1 order of magnitude larger than the equivalent experimental data, but the molecules' relative permeability coefficients are reproduced.
| Item Type: | Article |
|---|---|
| ISSN: | 1520-6106 (print) |
| Uncontrolled Keywords: | dynamics simulation, surface-area, phospholipid-bilayers, lecithin, bilayers, nonelectrolyte partition, dimyristoyl lecithin, transportphenomena, rapid calculation, solute diffusion, water transport |
| Related URLs: | http://dx.doi.org/10.1021/jp035260s |
| Subjects: | R Medicine > RM Therapeutics. Pharmacology Q Science > QH Natural history > QH301 Biology Q Science > QA Mathematics > QA76 Computer software |
| Divisions: | University Structure - Pre August 2011 > School of Chemistry |
| ePrint ID: | 20131 |
| URI: | http://eprints.soton.ac.uk/id/eprint/20131 |
| Deposited On: | 22 Feb 2006 |
| Last Modified: | 01 Jun 2011 09:35 |
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